Supplementary materials

Viral-encoded reverse transcriptase (RT) is a key component in replication (reverse transcribing viruses, generating complementary DNA from an RNA template) and genomic mutations (bacteriophage diversity-generating retroelement). However, the diversity of viral RTs remains poorly understood. Here, we identified 76,208 viral-derived RTs from publicly available genomic and metagenomic datasets to establish 13 viral-derived RT clusters (RTCs), belonging to six phylogenetic RT super clades. These include two viral-derived RT phylogenetic clades that have a close relationship with bacterial Retrons-like and Group II Introns-like RT. Phylogenetic inference of viral terminase-related proteins has revealed the differentiated evolutionary status of RTVs from various RT phylogenetic clades. The genome-content-based network suggests that RTVs tend to form independent clusters compared to other caudoviruses. Most RTVs are colonized in host-associated environments, with Bacteroidota, Bacillota, and Pseudomonadota being the main host lineages. The integrated RTVs were shared between multiple bacterial genera of Bacteroidota and Bacillota. The integrated RTVs from Pseudomonadota are genus-specific. Our results highlight the neglected diversity of RTVs and their potential host spectrums.